Compared with the previous full-waveform data, the new generation of ICESat-2/ATLAS (Advanced Terrain Laser Altimeter System) has a larger footprint overlap density and a smaller footprint area. This study used ATLAS data to estimate forest aboveground biomass (AGB) in a high-altitude, ecologically fragile area. The paper used ATLAS data as the main information source and a typical mountainous area in Shangri-La, northwestern Yunnan Province, China, as the study area. Then, we combined biomass data from 54 ground samples to obtain the estimated AGB of 74,873 footprints using a hyperparametric optimized random forest (RF) model. The total AGB was estimated by combining the best variance function model in geostatistics with the slope that is the covariates. The results showed that among the 50 index parameters and three topographic variables extracted based on ATLAS, six variables showed a significant correlation with AGB. They were, in order, number of canopy photons, Landsat percentage canopy, canopy photon rate, slope, number of photons, and apparent surface reflectance. The optimized random forest model was used to estimate the AGB within the footprints. The model accuracy was the coefficient of determination (R2) = 0.93, the root mean square error (RMSE) = 10.13 t/hm2, and the population estimation accuracy was 83.3%. The optimized model has a good estimation effect and can be used for footprint AGB estimation. The spatial structure analysis of the variance function of footprint AGB showed that the spherical model had the largest fitting accuracy (R2 = 0.65, the residual sum of squares (RSS) = 2.65 × 10−4), the nugget (C0) was 0.21, and the spatial structure ratio was 94.0%. It showed that the AGB of footprints had strong spatial correlation and could be interpolated by kriging. Finally, the slope in the topographic variables was selected as the co-interpolation variable, and cokriging spatial interpolation was performed. Furthermore, a continuous map of AGB spatial distribution was obtained, and the total AGB was 6.07 × 107 t. The spatial distribution of AGB showed the same trend as the distribution of forest stock. The absolute accuracy of the estimation was 82.6%, using the statistical value of the forest resource planning and design survey as a reference. The ATLAS data can improve the accuracy of AGB estimation in mountain forests. © 2022 by the authors.